Transcript Andrew Farmer NCGR Paul Scott Iowa State Bill

mRNA Transcript Expression in the
Ear Shoot Apical Meristem
and Correlation with Yield
A Translational Genomics Experiment
Utilizing Next-Generation
Sequencing Technology
And the B73 Genome Reference
Sequence
GENETIC MATERIALS
Four homozygous lines: Ex-PVP Accessions
Very similar in rate of development
(1) LH1
(2) PHG39
(3) LH123HT
(4) PHG84
Six F1 Hybrids
Six F2 Families
Twelve Reciprocal BC1 Families: A*B/A; A*B/B
Provides the entries for a generation means design
for the partition of genotypic variation into additive, dominance,
and inter-gametic epistatic genetic effects
EXPERIMENTAL DESIGN
Ear Shoot
Sampling
Ear Trait
Phenotyping
Ear Trait
Phenotyping
Ear Shoot
Sampling
BC1
BC1
F2
F2
Parents
Parents
F1
F1
Rep 1 BC1’
F1
F2
BC1’
F1
F2
Ear Shoot
Sampling
Ear Trait
Phenotyping
Parents
Parents
F2
F2
Rep 3 BC1’
BC1
F1
BC1’
BC1
F1
Rep 2 Parents
BC1’
BC1
Parents
BC1’
BC1
• Generations blocked separately so as to
eliminate unequal interplot competition
effects due to differences in vigor and rate
of development.
• Ear shoot sampling and ear trait phenoTyping blocked separately so as to provide
Normal ear development on intact plants.
• Sequencing and bioinformatics done on
extracted mRNA by National Center for
Genome Resources.
TRAIT WEIGHTS ON FIRST PRINCIPAL
COMPONENT OF GENOTYPIC VARIATION IN
THE MATURE EAR
0.50
First principal component
accounts for 90% of the variation
in ear traits
Variation primarily
Non-additive
0.40
0.30
0.20
0.10
Kernels
Per Row
Grain
Weight
Ear
Weight
Grain
Fill
Cob
Length
Cob
Weight
18,000
FREQUENCY DISTRIBUTION OF
TRANSCRIPT EXPRESSION GENETIC
EFFECTS AT FDR<=0.10
15,000
12,000
9,000
6,000
3,000
Genotypic
Additive
Dominance
InterGametic
Epistatic
Residual
Genetic
PERCENT OVER-REPRESENTATION OF GENES WITH
TRANSCRIPT EXPRESSION SIGNIFICANTLY CORRELATED
WITH KPR COMPONENT BY FUNCTIONAL CATEGORY
60
50
40
30
20
10
OxidoReductase
Transcription
Factors
Heat Shock
Stress Response
All
Others
RANK CORRELATIONS OF GENE
EXPRESSION WITH KERNELS PER ROW
COMPONENT CCAAT cAMP
Enhancer
Binding
Protein
Responsive
Element
Binding
C/EBP
CREB
1.0
0.5
0
-0.5
-1.0
Ramosa1 Ramosa2 Ramosa3 Ramosa3
Chr 2
Chr 7
Homeolog
Ramosa 1
Ramosa2
Ramosa3 homeolog
Knox 1 ELK
Pyruvate dehydrogenase
Transketolase
Tubby
C/EBP
N=394
Biosynthesis
r>=0.82
r=1
Kernels per row
r 1
CREB
Superoxide dismutase
Detox proteins (several)
Haem peroxidases (several)
NADH plastoquinone
Iron-sulfur protein
AMP-dependent synthetase
Adenine translocator
AP2/EREPB
r=-1
r<=-0.82
N=451
Generation of Reactive Oxygen
Species (ROS) DueTo OxidoReductase Activity During
Mitochondrial Respiration
SUMMARY
• Variation in genotypic expression of the
ramosa genes in the ear shoot spikeletpair meristem is highly correlated with
genotypic variation in kernels per row
in the mature ear.
• Reactive oxygen species may serve as a
signal acting on a gene network
centered on C/EBP and CREB that
regulates initiation of axillary branches
in the spikelet-pair meristem.
ACKNOWLEGEMENTS
Andrew Farmer NCGR
Paul Scott Iowa State
Bill Beavis Iowa State
Bob Schmidt UCSD
Sarah Hake & Maize Infl. Group
Adrienne Lauter Iowa State
Greg May NCGR
Kendall Lamkey Iowa State
QUESTIONS & COMMENTS
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